Maize genome 'dark matter' discovery a boon for breeders

Cornell and Florida State University researchers report they have identified 1 to 2 percent of the maize genome that turns genes on and off.

For astronomers, “dark matter” is the largely hypothetical substance that accounts for approximately 85 percent of the matter in the universe. Now, plant scientists have discovered a different kind of “dark matter” in the maize genome: a tiny percentage of regulatory DNA that accounts for roughly half of the variation in observable traits found in corn.

In a landmark finding, Cornell and Florida State University researchers report they have identified 1 to 2 percent of the maize genome that turns genes on and off, so they may now focus their attention on these areas for more efficient plant breeding.

“It allows us to start pinpointing the single base pair changes [small mutations] that are regulating or allowing plants to adapt to their environment. It helps us narrow down the hunt dramatically,” said Edward Buckler, a Cornell and U.S. Department of Agriculture (USDA) research geneticist and a co-author of the paper appearing May 16 in Proceedings of the National Academy of Sciences. Eli Rodgers-Melnick, a former postdoctoral researcher in Buckler’s lab currently with Pioneer, is the paper’s first author. Daniel Vera, director of the Center for Genomics and Personalized Medicine, and Hank Bass, an associate professor of biology, both at Florida State University, are co-authors.

Most DNA, including all the genes that code for proteins, is tightly coiled up to fit inside the nuclei of cells. For example, if you stretched DNA strands found in one human or corn cell all the way out, they would measure 2 meters. Yet when coiled in a nucleus, the genetic material is compacted nearly a millionfold. But there are also regions of DNA that are not tightly wrapped, known as “open chromatin.”

The researchers identified areas of open chromatin that regulate genes. The discovery was made possible by a single cost-effective chromatin profiling procedure to measure how tightly wrapped DNA is everywhere in the genome, developed by Vera and Bass.

“This assay costs about $20,000 and tells you the 1 percent of the genome that is really the most important for turning genes on and off,” said Buckler. While the half-a-billion dollar human Encyclopedia of DNA Elements (ENCODE) consortium pioneered many of this class of assays, this new assay is so efficient in pinpointing important regions in the DNA that the team expects it could be a transformative technique applicable to hundreds of crops.

Buckler’s lab has collected close to 15 years of data on how maize varieties grow in many types of field conditions, and the team used these data with the new assay to determine that about half of all the observable traits (phenotypes) seen in the field – such as yield, drought and stress tolerance, or starch content – could be mapped to regulatory DNA found in open chromatin, with the other half coming from genes.

Together, these two classes of DNA make up only about 3 percent of the total genome, allowing researchers and plant breeders to use genetic markers linked to these key genomic areas and new genomic editing techniques to accelerate maize breeding to meet demands of growing populations and climate changes.

By comparison, regulatory open chromatin regions may be as much as 8 percent of the genome in humans. In maize, the researchers had some early evidence that these regulatory regions might cover as much as 15 percent of the genome. “What was surprising was it turned out to be much smaller, only about 1 percent,” Buckler said.

“For me, it was the first time when the biology of the genome got simpler,” Buckler said. “Normally, we are always talking about how it’s so complex, but this time, it finally got simpler.”